5EXB

Wild type green fluorescent protein DendFP (Dendronephthya sp.)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms.

Pletneva, N.V.Pletnev, S.Pakhomov, A.A.Chertkova, R.V.Martynov, V.I.Muslinkina, L.Dauter, Z.Pletnev, V.Z.

(2016) Acta Crystallogr D Struct Biol 72: 922-932

  • DOI: https://doi.org/10.1107/S205979831601038X
  • Primary Citation of Related Structures:  
    5EXB, 5EXC

  • PubMed Abstract: 

    The fluorescent protein from Dendronephthya sp. (DendFP) is a member of the Kaede-like group of photoconvertible fluorescent proteins with a His62-Tyr63-Gly64 chromophore-forming sequence. Upon irradiation with UV and blue light, the fluorescence of DendFP irreversibly changes from green (506 nm) to red (578 nm). The photoconversion is accompanied by cleavage of the peptide backbone at the C(α)-N bond of His62 and the formation of a terminal carboxamide group at the preceding Leu61. The resulting double C(α)=C(β) bond in His62 extends the conjugation of the chromophore π system to include imidazole, providing the red fluorescence. Here, the three-dimensional structures of native green and photoconverted red forms of DendFP determined at 1.81 and 2.14 Å resolution, respectively, are reported. This is the first structure of photoconverted red DendFP to be reported to date. The structure-based mutagenesis of DendFP revealed an important role of positions 142 and 193: replacement of the original Ser142 and His193 caused a moderate red shift in the fluorescence and a considerable increase in the photoconversion rate. It was demonstrated that hydrogen bonding of the chromophore to the Gln116 and Ser105 cluster is crucial for variation of the photoconversion rate. The single replacement Gln116Asn disrupts the hydrogen bonding of Gln116 to the chromophore, resulting in a 30-fold decrease in the photoconversion rate, which was partially restored by a further Ser105Asn replacement.


  • Organizational Affiliation

    Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
232Dendronephthya sp.Mutation(s): 1 
UniProt
Find proteins for Q8T6U0 (Dendronephthya sp. SSAL-2002)
Explore Q8T6U0 
Go to UniProtKB:  Q8T6U0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8T6U0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
5SQ
Query on 5SQ
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC17 H17 N5 O4HIS, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.384α = 109.68
b = 106.397β = 100.01
c = 137.209γ = 101.72
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation14-14-00281

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2016-08-17
    Changes: Database references
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2021-09-08
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-11-06
    Changes: Structure summary